September 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 694fac: Implement on random validator ``split``.
by GitHub 15 Sep '16

15 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 694fac5f567491471dadd11bb934dbec5746cafd https://github.com/galaxyproject/galaxy/commit/694fac5f567491471dadd11bb934… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Implement on random validator ``split``. Commit: f34ab79d22b261e6606ae994f7c2b8bb14273ca2 https://github.com/galaxyproject/galaxy/commit/f34ab79d22b261e6606ae994f7c2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #2921 from jmchilton/implement_split Implement ``split`` on a validator. Compare: https://github.com/galaxyproject/galaxy/compare/c576f27d4fba...f34ab79d22b2

1 0

[galaxyproject/galaxy] a698fa: Update the Copyright year in the LICENSE.txt.
by GitHub 15 Sep '16

15 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a698fa52b3aef236cbf6bad729e286552b84114c https://github.com/galaxyproject/galaxy/commit/a698fa52b3aef236cbf6bad729e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE.txt Log Message: ----------- Update the Copyright year in the LICENSE.txt. Commit: c576f27d4fba92c1066964fc1b32d24921a65771 https://github.com/galaxyproject/galaxy/commit/c576f27d4fba92c1066964fc1b32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE.txt Log Message: ----------- Merge pull request #2926 from jmchilton/copyright Update the Copyright year in the LICENSE.txt. Compare: https://github.com/galaxyproject/galaxy/compare/e76bbf53b62f...c576f27d4fba

1 0

[galaxyproject/galaxy] 646428: Remove change handler for data and collection mult...
by GitHub 15 Sep '16

15 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove change handler for data and collection multiinput selectors in old run workflow form Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2920 from guerler/fix_collection_refresh [16.07] Prevent refresh for collection selector in old run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/b399c086254f...67a3cf34ca0e

1 0

[galaxyproject/galaxy] 21ccf7: API, history contents: contents download endpoint
by GitHub 15 Sep '16

15 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21ccf76b1009301365171d7a33afb380b40dd3a3 https://github.com/galaxyproject/galaxy/commit/21ccf76b1009301365171d7a33af… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- API, history contents: contents download endpoint - Adds an api endpoint at 'histories/{id}/contents/archive' for creating an archive from all history contents or a filtered subset of contents - Contents are returned in 'tgz' format currently - Datasets are located in the archive in paths roughly matching the nesting relationships of their parent collections - Filters can be applied using the same syntax as index - Adding 'dry_run=True' will return a JSON list of archive paths and dataset file paths for debugging - Adds map_datasets method for walking the datasets of histories and HDCAs Commit: e76bbf53b62f29f2d05459ecea13fd8e98449aa4 https://github.com/galaxyproject/galaxy/commit/e76bbf53b62f29f2d05459ecea13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2885 from carlfeberhard/file-walker API, history contents: contents download endpoint Compare: https://github.com/galaxyproject/galaxy/compare/f553d387a47d...e76bbf53b62f

1 0

[galaxyproject/galaxy] de763b: Initial commit to get working BBI reader into Trac...
by GitHub 15 Sep '16

15 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de763bedee23494035752c11abc5a62e26364e47 https://github.com/galaxyproject/galaxy/commit/de763bedee23494035752c11abc5… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/tracks.js A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/tracks.js.map A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Initial commit to get working BBI reader into Trackster. Commit: cdc82ef2f8d3f7c6c1f5e274fc5896f8e6e7aa48 https://github.com/galaxyproject/galaxy/commit/cdc82ef2f8d3f7c6c1f5e274fc58… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/queues.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/update_repository_manager.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako M test/base/interactor.py A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml Log Message: ----------- Merge branch 'dev' into bbi-js3 Commit: d99cbd79b61005b90ec5871fd90cec113d0ed21e https://github.com/galaxyproject/galaxy/commit/d99cbd79b61005b90ec5871fd90c… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/galaxy.ini.sample M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/util/postfork.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge branch 'dev' into bbi-js3 Commit: 41d0ee4f4392d188ec9ededa35391ef592213608 https://github.com/galaxyproject/galaxy/commit/41d0ee4f4392d188ec9ededa3539… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M client/galaxy/scripts/libs/bbi/bigwig.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/libs/bbi/bigwig.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/libs/bbi/bigwig.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Bring data provided by data manager in line with Trackster's bigwig datatype. Also allow LinePainter to draw regions of variable length. Commit: 74be6955b3c73feb5db6fc2ee0c66179672f8a6f https://github.com/galaxyproject/galaxy/commit/74be6955b3c73feb5db6fc2ee0c6… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Detect whether server has byte-range support and set LineTrack data manager appropriately. Commit: 7b44cc5470728b59a2b47c64aedd27774706dd8b https://github.com/galaxyproject/galaxy/commit/7b44cc5470728b59a2b47c64aedd… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js A config/plugins/visualizations/charts/static/charts/others/example/config.js A config/plugins/visualizations/charts/static/charts/others/example/logo.png A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js A config/plugins/visualizations/charts/static/components/jobs.js A config/plugins/visualizations/charts/static/components/model.js A config/plugins/visualizations/charts/static/components/screenshot.js A config/plugins/visualizations/charts/static/components/storage.js R config/plugins/visualizations/charts/static/library/datasets.js R config/plugins/visualizations/charts/static/library/jobs.js R config/plugins/visualizations/charts/static/library/screenshot.js R config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/models/chart.js R config/plugins/visualizations/charts/static/models/config.js A config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/bootstrap_history.py M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/utils/utils.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/index.mako A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js Log Message: ----------- Merge branch 'dev' into bbi-js3 Commit: 5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95 https://github.com/galaxyproject/galaxy/commit/5518c20a20e6fc38ac1edfbbdaa2… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Cleanup: (a) remove debugging statements; (b) use Galaxy app; and (c) fix offset issue for LinePainter using floor instead of ceil. Commit: f553d387a47d0ef1a58a1522c0f437e3b1783a59 https://github.com/galaxyproject/galaxy/commit/f553d387a47d0ef1a58a1522c0f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2880 from jgoecks/bbi-js3 Trackster: Read numerical data directly from bigwig files Compare: https://github.com/galaxyproject/galaxy/compare/921933ea9cb1...f553d387a47d

1 0

[galaxyproject/galaxy] 8616c0: Log the resolved dependency type
by GitHub 14 Sep '16

14 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 8616c0e87c055ed8e41563625498818a76769b2f https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e41563625498… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9 https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Merge pull request #2918 from martenson/pick-dep-log [16.07] cherry pick logging the resolved dependency type Compare: https://github.com/galaxyproject/galaxy/compare/e5f4f2fab6ce...b399c086254f

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 14 Sep '16

14 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85 https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 921933ea9cb108a45f804f36adc0dc76d447ed11 https://github.com/galaxyproject/galaxy/commit/921933ea9cb108a45f804f36adc0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/63f758f9976b...921933ea9cb1

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 14 Sep '16

14 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85 https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/c01ce21e2cdb...e5f4f2fab6ce

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 14 Sep '16

14 Sep '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5 https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/3492e96574ea...b50d07d5bf12

1 0

[galaxyproject/galaxy] 91a190: Datasets: allow admin to serialize permissions
by GitHub 14 Sep '16

14 Sep '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: allow admin to serialize permissions And updates tests. Commit: b88035955d7a81ff43858f092924b60bef1bca9c https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: confirm admin ability to set permissions The power was inside you all along. Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce13… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Permissions, datasets: allow admin in RBAC - Admin are considered permitted when calling ** dataset_manager.permssions.access and ** dataset_manager.permissions.manage - Update bad test - Add admin test to other permission checks Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon access/manage Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2 https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M test/unit/managers/test_DatasetManager.py Log Message: ----------- Datasets: test for anon deserialization Commit: b301fd42021245f5c3c7291207510659aa66b5ac https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c729120751… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Dataset perms: correct comment Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #2912 from carlfeberhard/dataset.admin-permissions [16.01] Allow admin to serialize/deserialize dataset permissions Compare: https://github.com/galaxyproject/galaxy/compare/68f718d53bc6...8bf7256ca8ec

1 0